Commit 7439f3d4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix typo

parent fe78d034
......@@ -61,12 +61,12 @@ class GatkVariantcalling(val root: Configurable) extends QScript with BiopetQScr
if (files.size == 1) return files
if (files.isEmpty) throw new IllegalStateException("Files can't be empty")
if (!doublePreProces.get) return files
val markDub = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
add(markDub, isIntermediate = useIndelRealigner)
val markDup = MarkDuplicates(this, files, new File(outputDir + outputName + ".dedup.bam"))
add(markDup, isIntermediate = useIndelRealigner)
if (useIndelRealigner) {
List(addIndelRealign(markDub.output, outputDir, isIntermediate = false))
List(addIndelRealign(markDup.output, outputDir, isIntermediate = false))
} else {
List(markDub.output)
List(markDup.output)
}
}
......
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